Despite being considered as a key instrument of the agricultural development policy, the investment support has received only limited attention in the Czech economic literature. The objective of this paper is to assess economic effects of the measure 121 “Modernisation of Agricultural Holdings” of the RDP 2007-2013 on the Czech farms. A particular focus is on the distribution of the supports and differentiated impacts of the supports according to the production conditions and farm size. The counterfactual approach is adopted, deploying direct matching algorithm with the treatment of hereoscedasticity. We show significant benefits of the investment support in terms of business expansion (represented by Gross value added) and labour productivity improvements. Analysing the sample of applicants for Measure 121 we show that large farms get much larger support than smaller farms. By splitting the sample by natural conditions and by size we demonstrate that benefits are higher on farms in less favoured areas and on medium-size farms in both the absolute and relative terms. Investigating the changes in bank indebtedness we yield an indication that on average the support mobilised additional resources to finance the sector investment. However, there is no statistically significant increase of bank indebtedness on large farms due to investment support. In turn, it can be interpreted that deadweight is rather high on large farms, while on average the deadweight of the investment support programme is rather low. Thus, the programme can improve its social efficiency if it is targeted to small and medium size farms.